data_6LFZ # _model_server_result.job_id qCInmUryuS84Bj3v9in--g _model_server_result.datetime_utc '2024-12-22 06:27:51' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 6lfz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":500}' # _entry.id 6LFZ # _exptl.entry_id 6LFZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 6LFZ _cell.length_a 107.287 _cell.length_b 216.953 _cell.length_c 104.705 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6LFZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N # _chem_comp.formula 'C15 H24 N2 O17 P2' _chem_comp.formula_weight 566.302 _chem_comp.id UPG _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER" # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag N1 C2 UPG sing 358 n n N1 C6 UPG sing 359 n n N1 C1C UPG sing 360 n n C2 N3 UPG sing 361 n n C2 O2 UPG doub 362 n n N3 C4 UPG sing 363 n n N3 HN3 UPG sing 364 n n C4 C5 UPG sing 365 n n C4 O4 UPG doub 366 n n C5 C6 UPG doub 367 n n C5 H5 UPG sing 368 n n C6 H6 UPG sing 369 n n C1C C2C UPG sing 370 n n C1C O4C UPG sing 371 n n C1C H1C UPG sing 372 n n C2C O2C UPG sing 373 n n C2C C3C UPG sing 374 n n C2C H2C UPG sing 375 n n O2C HO2C UPG sing 376 n n C3C C4C UPG sing 377 n n C3C O3C UPG sing 378 n n C3C H3C UPG sing 379 n n C4C O4C UPG sing 380 n n C4C C5C UPG sing 381 n n C4C H4C UPG sing 382 n n O3C HO3C UPG sing 383 n n C5C O5C UPG sing 384 n n C5C H5C1 UPG sing 385 n n C5C H5C2 UPG sing 386 n n O5C PA UPG sing 387 n n PA O1A UPG doub 388 n n PA O2A UPG sing 389 n n PA O3A UPG sing 390 n n O2A HOA2 UPG sing 391 n n O3A PB UPG sing 392 n n PB O1B UPG doub 393 n n PB O2B UPG sing 394 n n PB O3B UPG sing 395 n n O2B HOB2 UPG sing 396 n n O3B C1' UPG sing 397 n n C1' C2' UPG sing 398 n n C1' O5' UPG sing 399 n n C1' H1' UPG sing 400 n n C2' C3' UPG sing 401 n n C2' O2' UPG sing 402 n n C2' H2' UPG sing 403 n n C3' C4' UPG sing 404 n n C3' O3' UPG sing 405 n n C3' H3' UPG sing 406 n n C4' C5' UPG sing 407 n n C4' O4' UPG sing 408 n n C4' H4' UPG sing 409 n n C5' C6' UPG sing 410 n n C5' O5' UPG sing 411 n n C5' H5' UPG sing 412 n n C6' O6' UPG sing 413 n n C6' "H6'1" UPG sing 414 n n C6' "H6'2" UPG sing 415 n n O2' HO2' UPG sing 416 n n O3' HO3' UPG sing 417 n n O4' HO4' UPG sing 418 n n O6' HO6' UPG sing 419 n n # _atom_sites.entry_id 6LFZ _atom_sites.fract_transf_matrix[1][1] 0.009321 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004609 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.009551 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 UPG A 1 500 500 UPG UPG . D 2 UPG B 1 500 500 UPG UPG . E 3 HOH A 1 601 24 HOH HOH . E 3 HOH A 2 602 21 HOH HOH . E 3 HOH A 3 603 8 HOH HOH . E 3 HOH A 4 604 16 HOH HOH . E 3 HOH A 5 605 7 HOH HOH . E 3 HOH A 6 606 22 HOH HOH . E 3 HOH A 7 607 23 HOH HOH . E 3 HOH A 8 608 26 HOH HOH . E 3 HOH A 9 609 5 HOH HOH . E 3 HOH A 10 610 32 HOH HOH . E 3 HOH A 11 611 30 HOH HOH . E 3 HOH A 12 612 14 HOH HOH . E 3 HOH A 13 613 28 HOH HOH . E 3 HOH A 14 614 25 HOH HOH . E 3 HOH A 15 615 48 HOH HOH . E 3 HOH A 16 616 13 HOH HOH . E 3 HOH A 17 617 34 HOH HOH . E 3 HOH A 18 618 20 HOH HOH . E 3 HOH A 19 619 11 HOH HOH . E 3 HOH A 20 620 29 HOH HOH . E 3 HOH A 21 621 31 HOH HOH . E 3 HOH A 22 622 18 HOH HOH . E 3 HOH A 23 623 1 HOH HOH . E 3 HOH A 24 624 15 HOH HOH . E 3 HOH A 25 625 10 HOH HOH . E 3 HOH A 26 626 37 HOH HOH . E 3 HOH A 27 627 17 HOH HOH . E 3 HOH A 28 628 35 HOH HOH . E 3 HOH A 29 629 6 HOH HOH . E 3 HOH A 30 630 19 HOH HOH . E 3 HOH A 31 631 49 HOH HOH . E 3 HOH A 32 632 27 HOH HOH . E 3 HOH A 33 633 9 HOH HOH . E 3 HOH A 34 634 12 HOH HOH . F 3 HOH B 1 601 44 HOH HOH . F 3 HOH B 2 602 46 HOH HOH . F 3 HOH B 3 603 4 HOH HOH . F 3 HOH B 4 604 40 HOH HOH . F 3 HOH B 5 605 43 HOH HOH . F 3 HOH B 6 606 36 HOH HOH . F 3 HOH B 7 607 41 HOH HOH . F 3 HOH B 8 608 53 HOH HOH . F 3 HOH B 9 609 33 HOH HOH . F 3 HOH B 10 610 38 HOH HOH . F 3 HOH B 11 611 45 HOH HOH . F 3 HOH B 12 612 54 HOH HOH . F 3 HOH B 13 613 3 HOH HOH . F 3 HOH B 14 614 52 HOH HOH . F 3 HOH B 15 615 42 HOH HOH . F 3 HOH B 16 616 39 HOH HOH . F 3 HOH B 17 617 50 HOH HOH . F 3 HOH B 18 618 47 HOH HOH . F 3 HOH B 19 619 51 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N1 UPG . . . C 2 1.252 -34.27 1.404 1 55.2 ? N1 UPG 500 A 1 HETATM 2 C C2 UPG . . . C 2 2.349 -34.398 0.567 1 55.2 ? C2 UPG 500 A 1 HETATM 3 N N3 UPG . . . C 2 3.443 -35.021 0.951 1 55.2 ? N3 UPG 500 A 1 HETATM 4 C C4 UPG . . . C 2 3.506 -35.518 2.168 1 55.2 ? C4 UPG 500 A 1 HETATM 5 C C5 UPG . . . C 2 2.44 -35.395 3.026 1 55.2 ? C5 UPG 500 A 1 HETATM 6 C C6 UPG . . . C 2 1.3 -34.743 2.627 1 55.2 ? C6 UPG 500 A 1 HETATM 7 O O2 UPG . . . C 2 2.289 -33.932 -0.565 1 55.2 ? O2 UPG 500 A 1 HETATM 8 O O4 UPG . . . C 2 4.53 -36.099 2.537 1 55.2 ? O4 UPG 500 A 1 HETATM 9 C C1C UPG . . . C 2 0.077 -33.568 0.931 1 55.2 ? C1C UPG 500 A 1 HETATM 10 C C2C UPG . . . C 2 -0.816 -34.579 0.262 1 55.2 ? C2C UPG 500 A 1 HETATM 11 O O2C UPG . . . C 2 -0.656 -34.547 -1.158 1 57.22 ? O2C UPG 500 A 1 HETATM 12 C C3C UPG . . . C 2 -2.212 -34.214 0.697 1 55.2 ? C3C UPG 500 A 1 HETATM 13 C C4C UPG . . . C 2 -2.041 -33.305 1.877 1 55.2 ? C4C UPG 500 A 1 HETATM 14 O O4C UPG . . . C 2 -0.664 -33.084 2.034 1 55.2 ? O4C UPG 500 A 1 HETATM 15 O O3C UPG . . . C 2 -2.926 -33.517 -0.311 1 55.2 ? O3C UPG 500 A 1 HETATM 16 C C5C UPG . . . C 2 -2.445 -34.084 3.091 1 55.2 ? C5C UPG 500 A 1 HETATM 17 O O5C UPG . . . C 2 -3.126 -33.284 4.021 1 55.2 ? O5C UPG 500 A 1 HETATM 18 P PA UPG . . . C 2 -4.196 -34.009 4.909 1 55.2 ? PA UPG 500 A 1 HETATM 19 O O1A UPG . . . C 2 -4.329 -35.387 4.39 1 55.2 ? O1A UPG 500 A 1 HETATM 20 O O2A UPG . . . C 2 -5.382 -33.142 4.939 1 55.2 ? O2A UPG 500 A 1 HETATM 21 O O3A UPG . . . C 2 -3.451 -34.111 6.326 1 55.2 ? O3A UPG 500 A 1 HETATM 22 P PB UPG . . . C 2 -2.915 -32.963 7.335 1 55.2 ? PB UPG 500 A 1 HETATM 23 O O1B UPG . . . C 2 -2.462 -31.766 6.571 1 55.2 ? O1B UPG 500 A 1 HETATM 24 O O2B UPG . . . C 2 -1.951 -33.563 8.304 1 55.2 ? O2B UPG 500 A 1 HETATM 25 O O3B UPG . . . C 2 -4.223 -32.586 8.176 1 69.6 ? O3B UPG 500 A 1 HETATM 26 C C1' UPG . . . C 2 -4.73 -31.284 8.479 1 61.11 ? C1' UPG 500 A 1 HETATM 27 C C2' UPG . . . C 2 -5.376 -31.373 9.85 1 59.64 ? C2' UPG 500 A 1 HETATM 28 C C3' UPG . . . C 2 -6.392 -32.507 9.852 1 57.19 ? C3' UPG 500 A 1 HETATM 29 C C4' UPG . . . C 2 -7.389 -32.29 8.722 1 57.08 ? C4' UPG 500 A 1 HETATM 30 C C5' UPG . . . C 2 -6.68 -32.019 7.414 1 55.2 ? C5' UPG 500 A 1 HETATM 31 C C6' UPG . . . C 2 -7.724 -31.618 6.421 1 55.2 ? C6' UPG 500 A 1 HETATM 32 O O2' UPG . . . C 2 -4.39 -31.587 10.867 1 55.93 ? O2' UPG 500 A 1 HETATM 33 O O3' UPG . . . C 2 -7.081 -32.498 11.106 1 55.2 ? O3' UPG 500 A 1 HETATM 34 O O4' UPG . . . C 2 -8.295 -33.387 8.559 1 55.2 ? O4' UPG 500 A 1 HETATM 35 O O5' UPG . . . C 2 -5.769 -30.937 7.572 1 55.2 ? O5' UPG 500 A 1 HETATM 36 O O6' UPG . . . C 2 -8.315 -30.485 7.038 1 57.96 ? O6' UPG 500 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 135 _model_server_stats.create_model_time_ms 59 _model_server_stats.query_time_ms 367 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 36 #